title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=799 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Removal of heavy oil from contaminated surfaces with a detergent formulation containing biosurfactants produced by Pseudomonas spp. link: https://peerj.com/articles/12518 last-modified: 2021-11-25 description: Industrial plants powered by heavy oil routinely experience problems with leaks in different parts of the system, such as during oil transport, the lubrication of equipment and mechanical failures. The surfactants, degreasing agents and solvents that make up detergents commonly used for cleaning grease-covered surfaces are synthetic, non-biodegradable and toxic, posing risks to the environment as well as the health of workers involved in the cleaning process. To address this problem, surfactant agents of a biodegradable nature and low toxicity, such as microbial surfactants, have been widely studied as an attractive, efficient solution to replace chemical surfactants in decontamination processes. In this work, the bacterial strains Pseudomonas cepacia CCT 6659, Pseudomonas aeruginosa UCP 0992, Pseudomonas aeruginosa ATCC 9027 and Pseudomonas aeruginosa ATCC 10145 were evaluated as biosurfactant producers in media containing different combinations and types of substrates and under different culture conditions. The biosurfactant produced by P. aeruginosa ATCC 10145 cultivated in a mineral medium composed of 5.0% glycerol and 2.0% glucose for 96 h was selected to formulate a biodetergent capable of removing heavy oil. The biosurfactant was able to reduce the surface tension of the medium to 26.40 mN/m, with a yield of approximately 12.00 g/L and a critical micelle concentration of 60.00 mg/L. The biosurfactant emulsified 97.40% and dispersed 98.00% of the motor oil. The detergent formulated with the biosurfactant also exhibited low toxicity in tests involving the microcrustacean Artemia salina and seeds of the vegetable Brassica oleracea. The detergent was compared to commercial formulations and removed 100% of the Special B1 Fuel Oil (OCB1) from different contaminated surfaces, demonstrating potential as a novel green remover with industrial applications. creator: Charles Bronzo B. Farias creator: Rita de Cássia F. Soares da Silva creator: Fabíola Carolina G. Almeida creator: Valdemir A. Santos creator: Leonie A. Sarubbo uri: https://doi.org/10.7717/peerj.12518 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Farias et al. title: Biogeographic evidence supports the Old Amazon hypothesis for the formation of the Amazon fluvial system link: https://peerj.com/articles/12533 last-modified: 2021-11-25 description: The Amazon has high biodiversity, which has been attributed to different geological events such as the formation of rivers. The Old and Young Amazon hypotheses have been proposed regarding the date of the formation of the Amazon basin. Different studies of historical biogeography support the Young Amazon model, however, most studies use secondary calibrations or are performed at the population level, preventing evaluation of a possible older formation of the Amazon basin. Here, we evaluated the fit of molecular phylogenetic and biogeographic data to previous models regarding the age of formation of the Amazon fluvial system. We reconstructed time-calibrated molecular phylogenies through Bayesian inference for six taxa belonging to Amphibia, Aves, Insecta and Mammalia, using both, nuclear and mitochondrial DNA sequence data and fossils as calibration points, and explored priors for both data sources. We detected the most plausible vicariant barriers for each phylogeny and performed an ancestral reconstruction analysis using areas bounded by major Amazonian rivers, and therefore, evaluated the effect of different dispersal rates over time based on geological and biogeographical information. The majority of the genes analyzed fit a relaxed clock model. The log normal distribution fits better and leads to more precise age estimations than the exponential distribution. The data suggested that the first dispersals to the Amazon basin occurred to Western Amazonia from 16.2–10.4 Ma, and the taxa covered most of the areas of the Amazon basin between 12.2–6.2 Ma. Additionally, regardless of the method, we obtained evidence for two rivers: Tocantins and Madeira, acting as vicariant barriers. Given the molecular and biogeographical analyses, we found that some taxa were fitted to the “Old Amazon” model. creator: Karen Méndez-Camacho creator: Omar Leon-Alvarado creator: Daniel R. Miranda-Esquivel uri: https://doi.org/10.7717/peerj.12533 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Méndez-Camacho et al. title: Gender specific eRNA TBX5-AS1 as the immunological biomarker for male patients with lung squamous cell carcinoma in pan-cancer screening link: https://peerj.com/articles/12536 last-modified: 2021-11-25 description: As an innate feature of human beings, gender differences have an influence on various biological phenotypes, yet it does not attract enough attention in genomics studies. The prognosis of multiple carcinomas usually exhibits a favorable ending for female patients, but the neglect of gender differences can cause serious bias in survival analysis. Enhancer RNAs (eRNAs) are mostly downstream of androgens or estrogen. The present study was aimed to screen eRNAs in patients with non-small-cell lung cancer. The findings revealed that eRNA TBX5-AS1 was expressed differently between female and male patients. Meanwhile, its prognostic significance appeared only in male patients with squamous cell carcinoma (SCC) type. The Gene Set Enrichment Analysis proved that the expression level of TBX5-AS1 increased following the activation of the androgen signaling pathway. In pan-cancer analysis, the prognostic prediction based on gender grouping obtained more meaningful results, and the synergy between TBX5-AS1 and its homologous target was more consistent. Furthermore, immunity variations between sexes prompted us to explore the role that TBX5-AS1 played in tumor microenvironment and immunotherapy. The robust evidence proved that male patients with high expression of TBX5-AS1 possessed a malignant immune microenvironment and urgently needed immune checkpoint inhibitor treatment. In conclusion, TBX5-AS1 may be one of the strongest candidates to predict prognosis for male patients with SCC and provide a reference for immunotherapy. creator: Tao Yan creator: Kai Wang creator: Qidi Zhao creator: Junjie Zhuang creator: Hongchang Shen creator: Guoyuan Ma creator: Lei Cong creator: Jiajun Du uri: https://doi.org/10.7717/peerj.12536 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yan et al. title: The tongue of the red panda (Ailurus fulgens fulgens Cuvier, 1825)—a stereoscopy, light microscopy and ultrastructural analysis link: https://peerj.com/articles/12559 last-modified: 2021-11-25 description: In the light of recent molecular studies, there are two phylogenetic species of the red panda (Ailurus fulgens): Ailurus fulgens fulgens and Ailurus fulgens styani. The red panda belongs to the endangered species living in the wild only in Asia and is included in the CITES list. Although the biology and diet of this species has been extensively described, the histological structure of the tongue and lingual glands has not yet been characterized in detail in relation to the lifestyle of this mammal under specific conditions and as a basis for comparative anatomical studies of the biodiversity of endemic species. Study samples were collected from two adult males of Ailurus fulgens f. held in Wrocław Zoological Garden. Both tongues were examined macroscopically; moreover, samples with lingual papillae for light microscopy and scanning electron microscopy (SEM) were collected from the apex, body and root of the tongue. Both tongues of the Ailurus fulgens f. males were approximately 9 cm long. The dorsal lingual surface was covered with mechanical and gustatory lingual papillae. Filiform papillae were observed on the apex and the body of the tongue, while small conical papillae were observed on the root of the tongue. An elongated, 1–1.5 cm long cylinder-shaped lyssa was observed in the ventral part of the apex. Moreover, most numerous and largest round in shape fungiform papillae were observed on the apex and on the border of the body and root of the tongue, located directly rostrally to 12–13 round and oval in shape vallate papillae. The SEM study showed that filiform papillae on the apex had several long secondary processes, while filiform papillae on the body of the tongue were taller and their secondary papillae were shorter than the equivalent structures on the apex of the tongue. The SEM study showed numerous taste pores on the surface of the fungiform papilla, while irregular surface of the vallate papillae, however some of them had smoother surface. Mixed glands (comprised of mucous acini and serous acini) were present within the vallum (within the connective tissue core) of the vallate papilla. Beneath the papillae more serous glands were observed, while the posterior lingual glands in the caudal part of the root of the tongue were mucoserous (mucous units were prevalent). A characteristic feature of the tongue of Ailurus fulgens f. was the presence of lyssa, which is comparable to other representatives of Carnivora, but the number of vallate papillae was individually variable. The lack of strongly developed mechanical conical papillae probably may be related to the type of plant food that is particularly dominant in red panda. Further differences between Ailurus fulgens f. and Ailurus fulgens s. cannot be excluded. The results of these studies may be useful especially for veterinarians specializing in working with exotic animals and people dealing with wildlife conservation. creator: Karolina Goździewska-Harłajczuk creator: Pavla Hamouzová creator: Joanna Klećkowska-Nawrot creator: Petr Čížek uri: https://doi.org/10.7717/peerj.12559 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Goździewska-Harłajczuk et al. title: A comparison of food sources of nudibranch mollusks at different depths off the Kuril Islands using fatty acid trophic markers link: https://peerj.com/articles/12336 last-modified: 2021-11-24 description: Gastropod molluscs such as nudibranchs are important members of deep-sea benthic ecosystems. However, data on the trophic ecology and feeding specialization of these animals are limited to date. The method of fatty acid trophic markers (FATM) was applied to determine the dietary preferences of nudibranchs off the Kuril Islands. Fatty acid (FA) compositions of Dendronotus sp., Tritonia tetraquetra, and Colga pacifica collected from deep waters were analyzed and compared with those of Aeolidia papillosa and Coryphella verrucosa from the offshore zone. The high level of FATM such as 22:5n-6 and C20 monounsaturated FAs indicated that Dendronotus sp. preys on sea anemones and/or anthoathecates hydroids similarly to that of shallow-water species A. papillosa and C. verrucosa. The high percentage of tetracosapolyenoic acids and the ratio 24:6n-3/24:5n-6 indicated that T. tetraquetra preys on soft corals such as Gersemia and/or Acanella at a depth of 250 m, but soft corals of the family Primnoidae may be the main item in the diet of T. tetraquetra at a depth of 500 m. The high content of Δ 7,13-22:2 and 22:6n-3 shows that C. pacifica can feed on bryozoans. In C. pacifica, 22:5n-6 may be synthesized intrinsically by the mollusks, whereas odd-chain and branched saturated FAs originate from associated bacteria. creator: Anatolii Komisarenko creator: Vladimir Mordukhovich creator: Irina Ekimova creator: Andrey Imbs uri: https://doi.org/10.7717/peerj.12336 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Komisarenko et al. title: Genome-wide QTL mapping of yield and agronomic traits in two widely adapted winter wheat cultivars from multiple mega-environments link: https://peerj.com/articles/12350 last-modified: 2021-11-24 description: Quantitative trait loci (QTL) analysis could help to identify suitable molecular markers for marker-assisted breeding (MAB). A mapping population of 124 F5:7recombinant inbred lines derived from the cross ‘TAM 112’/‘TAM 111’ was grown under 28 diverse environments and evaluated for grain yield, test weight, heading date, and plant height. The objective of this study was to detect QTL conferring grain yield and agronomic traits from multiple mega-environments. Through a linkage map with 5,948 single nucleotide polymorphisms (SNPs), 51 QTL were consistently identified in two or more environments or analyses. Ten QTL linked to two or more traits were also identified on chromosomes 1A, 1D, 4B, 4D, 6A, 7B, and 7D. Those QTL explained up to 13.3% of additive phenotypic variations with the additive logarithm of odds (LOD(A)) scores up to 11.2. The additive effect increased yield up to 8.16 and 6.57 g m−2 and increased test weight by 2.14 and 3.47 kg m−3 with favorable alleles from TAM 111 and TAM 112, respectively. Seven major QTL for yield and six for TW with one in common were of our interest on MAB as they explained 5% or more phenotypic variations through additive effects. This study confirmed previously identified loci and identified new QTL and the favorable alleles for improving grain yield and agronomic traits. creator: Smit Dhakal creator: Xiaoxiao Liu creator: Chenggen Chu creator: Yan Yang creator: Jackie C. Rudd creator: Amir M.H. Ibrahim creator: Qingwu Xue creator: Ravindra N. Devkota creator: Jason A. Baker creator: Shannon A. Baker creator: Bryan E. Simoneaux creator: Geraldine B. Opena creator: Russell Sutton creator: Kirk E. Jessup creator: Kele Hui creator: Shichen Wang creator: Charles D. Johnson creator: Richard P. Metz creator: Shuyu Liu uri: https://doi.org/10.7717/peerj.12350 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Dhakal et al. title: The structure and functional profile of ruminal microbiota in young and adult reindeers (Rangifer tarandus) consuming natural winter-spring and summer-autumn seasonal diets link: https://peerj.com/articles/12389 last-modified: 2021-11-24 description: BackgroundThe key natural area of Russian reindeer (Rangifer tarandus, Nenets breed) is arctic zones, with severe climatic conditions and scarce feed resources, especially in the cold winter season. The adaptation of reindeer to these conditions is associated not only with the genetic potential of the animal itself. The rumen microbiome provides significant assistance in adapting animals to difficult conditions by participating in the fiber digestion. The aim of our study is to investigate the taxonomy and predicted metabolic pathways of the ruminal microbiota (RM) during the winter–spring (WS) and summer–autumn (SA) seasons, in calves and adult reindeer inhabiting the natural pastures of the Yamalo-Nenetsky Autonomous District of the Russian Federation.MethodsThe RM in reindeer was studied using the Next Generation Sequencing method with the MiSeq (Illumina, San Diego, CA, USA) platform. Reconstruction and prediction of functional profiles of the metagenome, gene families, and enzymes were performed using the software package PICRUSt2 (v.2.3.0).ResultsThe nutritional value of WS and SA diets significantly differed. Crude fiber content in the WS diet was higher by 22.4% (p < 0.05), compared to SA, indicating possibly poorer digestibility and necessity of the adaptation of the RM to this seasonal change. A total of 22 bacterial superphyla and phyla were found in the rumen, superphylum Bacteroidota and phylum Firmicutes being the dominating taxa (up to 48.1% ± 4.30% and 46.1% ± 4.80%, respectively); while only two archaeal phyla presented as minor communities (no more then 0.54% ± 0.14% totally). The percentages of the dominating taxa were not affected by age or season. However, significant changes in certain minor communities were found, with seasonal changes being more significant than age-related ones. The percentage of phylum Actinobacteriota significantly increased (19.3-fold) in SA, compared to WS (p = 0.02) in adults, and the percentage of phylum Cyanobacteria increased up to seven-fold (p = 0.002) in adults and calves. Seasonal changes in RM can improve the ability of reindeer to withstand the seasons characterized by a low availability of nutrients. The PICRUSt2 results revealed 257 predicted metabolic pathways in RM: 41 pathways were significantly (p < 0.05) influenced by season and/or age, including the processes of synthesis of vitamins, volatile fatty acids, and pigments; metabolism of protein, lipids, and energy; pathogenesis, methanogenesis, butanediol to pyruvate biosynthesis, cell wall biosynthesis, degradation of neurotransmitters, lactic acid fermentation, and biosynthesis of nucleic acids. A large part of these changeable pathways (13 of 41) was related to the synthesis of vitamin K homologues.ConclusionThe results obtained improve our knowledge on the structure and possible metabolic pathways of the RM in reindeer, in relation to seasonal changes. creator: Elena Yildirim creator: Larisa Ilina creator: Georgy Laptev creator: Valentina Filippova creator: Evgeni Brazhnik creator: Timur Dunyashev creator: Andrey Dubrovin creator: Natalia Novikova creator: Daria Tiurina creator: Nikolay Tarlavin creator: Kasim Laishev uri: https://doi.org/10.7717/peerj.12389 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yildirim et al. title: The reporting of p values, confidence intervals and statistical significance in Preventive Veterinary Medicine (1997–2017) link: https://peerj.com/articles/12453 last-modified: 2021-11-24 description: BackgroundDespite much discussion in the epidemiologic literature surrounding the use of null hypothesis significance testing (NHST) for inferences, the reporting practices of veterinary researchers have not been examined. We conducted a survey of articles published in Preventive Veterinary Medicine, a leading veterinary epidemiology journal, aimed at (a) estimating the frequency of reporting p values, confidence intervals and statistical significance between 1997 and 2017, (b) determining whether this varies by article section and (c) determining whether this varies over time.MethodsWe used systematic cluster sampling to select 985 original research articles from issues published in March, June, September and December of each year of the study period. Using the survey data analysis menu in Stata, we estimated overall and yearly proportions of article sections (abstracts, results-texts, results-tables and discussions) reporting p values, confidence intervals and statistical significance. Additionally, we estimated the proportion of p values less than 0.05 reported in each section, the proportion of article sections in which p values were reported as inequalities, and the proportion of article sections in which confidence intervals were interpreted as if they were significance tests. Finally, we used Generalised Estimating Equations to estimate prevalence odds ratios and 95% confidence intervals, comparing the occurrence of each of the above-mentioned reporting elements in one article section relative to another.ResultsOver the 20-year period, for every 100 published manuscripts, 31 abstracts (95% CI [28–35]), 65 results-texts (95% CI [61–68]), 23 sets of results-tables (95% CI [20–27]) and 59 discussion sections (95% CI [56–63]) reported statistical significance at least once. Only in the case of results-tables, were the numbers reporting p values (48; 95% CI [44–51]), and confidence intervals (44; 95% CI [41–48]) higher than those reporting statistical significance. We also found that a substantial proportion of p values were reported as inequalities and most were less than 0.05. The odds of a p value being less than 0.05 (OR = 4.5; 95% CI [2.3–9.0]) or being reported as an inequality (OR = 3.2; 95% CI [1.3–7.6]) was higher in the abstracts than in the results-texts. Additionally, when confidence intervals were interpreted, on most occasions they were used as surrogates for significance tests. Overall, no time trends in reporting were observed for any of the three reporting elements over the study period.ConclusionsDespite the availability of superior approaches to statistical inference and abundant criticism of its use in the epidemiologic literature, NHST is substantially the most common means of inference in articles published in Preventive Veterinary Medicine. This pattern has not changed substantially between 1997 and 2017. creator: Locksley L. McV. Messam creator: Hsin-Yi Weng creator: Nicole W. Y. Rosenberger creator: Zhi Hao Tan creator: Stephanie D. M. Payet creator: Mahishi Santbakshsing uri: https://doi.org/10.7717/peerj.12453 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Messam et al. title: Characterization of the morphology and complete mitochondrial genomes of Eupteryx minusula and Eupteryx gracilirama (Hemiptera: Cicadellidae: Typhlocybinae) from Karst area, Southwest China link: https://peerj.com/articles/12501 last-modified: 2021-11-24 description: BackgroundThe hemipteran insect family Cicadellidae (leafhoppers) includes >2,600 valid genera and >22,000 valid species worldwide, including >2,000 species in China. Typhlocybinae, second largest subfamilies of Cicadellidae, is widely distributed in the six major zoogeographic regions of the world, including >4,000 species worldwide and >1,000 species in China. Previously, morphological analysis are often effective to the way of taxonomy, but it did not combine with molecular biology. Therefore, morphology and mitochondrial genomes (mitogenomes) of two leafhopper species, Eupteryx (Eupteryx) minusculaLindberg, 1929 and Eupteryx (Stacla) graciliramaHou, Zhang & Huang, 2016 were studied and analyzed. This study analyzed the morphological and molecular characteristics of the two leafhoppers, and showed whether the results of the two identifications were consistent.MethodsBased on the method of comparison, mitogenomes and morphology were analyzed to prove the relationship between the two leafhoppers.ResultsAlthough two focal species are classified in two different subgenera of the same genus, they still share many morphological features, such as the moderately produced crown fore margin; the milky yellow apical part of scutellum; the pronotum, basal triangles of scutellum, and forewing are dark with several colorless patches on the surface; the light yellow face, without any spots or stripes, and so on. The circular mitogenomes are 16,944 bp long in E. minuscula (GenBank: MN910279) and 17,173 bp long in E. gracilirama (GenBank: MT594485). All of the protein-coding genes are starting with ATN, except for some in mitogenome, which has a single T or TAN as a stop codon. All tRNAs have the typical cloverleaf-shaped structure except for trnS1 (AGN) (E. minuscula) which has a reduced DHU arm. Moreover, these two mitogenomes have trnR with an unpaired base in the acceptor stem. The phylogenetic relationships between E. minuscula and E. gracilirama in respect to related lineages were reconstructed using Maximum likelihood and Maximum parsimony analyses.DiscussionThe result showed that the tribe Typhlocybini is a sister to the tribes Erythroneurini and Empoascini, and five genera, Bolanusoides, Typhlocyba, Eupteryx, Zyginella and Limassolla are forming a single clade. E. minuscula and E. gracilirama are clustered together, supporting the monophyly of the genus Eupteryx. The above conclusions are consistent with the traditional classification of the subfamily. creator: Zhouwei Yuan creator: Kangning Xiong creator: Ni Zhang creator: Can Li creator: Yuehua Song uri: https://doi.org/10.7717/peerj.12501 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yuan et al. title: Proteomic profiling of the endogenous peptides of MRSA and MSSA link: https://peerj.com/articles/12508 last-modified: 2021-11-24 description: Staphylococcus aureus is a Gram-positive bacterium that can cause diverse skin and soft tissue infections. Methicillin-resistant Staphylococcus aureus (MRSA) can cause more severe infections than methicillin-susceptible Staphylococcus aureus (MSSA). Nevertheless, the physiological and metabolic regulation of MSSA and MRSA has not been well studied. In light of the increased interest in endogenous peptides and recognition of the important roles that they play, we studied the endogenous peptidome of MSSA and MRSA. We identified 1,065 endogenous peptides, among which 435 were differentially expressed (DE), with 292 MSSA-abundant endogenous peptides and 35 MRSA-abundant endogenous peptides. MSSA-abundant endogenous peptides have significantly enriched “VXXXK” motif of at the C-terminus. MSSA-abundant endogenous peptides are involved in penicillin-binding and immune responses, whereas MRSA-abundant endogenous peptides are associated with antibiotic resistance and increased toxicity. Our characterization of the peptidome of MSSA and MRSA provides a rich resource for future studies to explore the functional regulation of drug resistance in S. aureus and may also help elucidate the mechanisms of its pathogenicity and the development of treatments. creator: Haixia Tu creator: Fei Xu creator: Yiwei Cheng creator: Qianglong Pan creator: Xiao Cai creator: Shouxing Wang creator: Shuting Ge creator: Min Cao creator: Dongming Su creator: Yan Li uri: https://doi.org/10.7717/peerj.12508 license: https://creativecommons.org/licenses/by-nc/4.0/ rights: ©2021 Tu et al.